Abstract
Motivation: Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance.
Results: We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases). Using the ClinVar benchmark, CADD was the best tool for detecting the pathogenic variants that are mainly located in protein coding gene regions. Using the COSMIC benchmark, FATHMM-MKL, GWAVA and SOMliver outperformed the other tools for pathogenic variants that are typically located in lincRNAs, pseudogenes, and other parts of the non-coding genome. However, all tools had low precision, which could potentially be improved by future non-coding genome feature discoveries. These results may have been influenced by the presence of potential benign variants in the COSMIC database. The development of a gold standard as consistent as ClinVar for these regions will be necessary to confirm our tool ranking.
Availability and Implementation: The Snakemake, C ++ and R codes are freely available from https://github.com/Oncostat/BenchmarkNCVTools and supported on Linux.
Contact: damien.drubay@gustaveroussy.fr.
Supplementary information: Supplementary results are available at Bioinformatics online.

Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids.

RNA. 2017 02;23(2):229-239

Authors: Lehmann J

Abstract
The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An induced-fit mechanism has been uncovered in the PTC, but a possible connection between this mechanism and the uniform handling of the substrates has not been investigated. We present an analysis of published ribosome structures supporting the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. We show that this hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Our analysis reveals that induction constrains the amino acids into a reactive conformation in a side-chain independent manner. It allows us to highlight the rationale of the PTC structural organization, which confers to the ribosome the very unusual ability to handle large as well as small substrates.

Abstract
We examine whether the frequency of amino acids across an organism's proteome is primarily determined by optimization to function or other factors, such as the structure of the genetic code. Considering all available proteins together, we first point out that the frequency of an amino acid in a proteome negatively correlates with its mass, suggesting that the genome preserves a fundamental distribution ruled by simple energetics. Given the universality of such distributions, one can use outliers, cysteine and leucine, to identify amino acids that deviate from this simple rule for functional purposes and examine those functions. We quantify the strength of such selection as the entropic cost outliers pay to defy the mass-frequency relation. Codon degeneracy of an amino acid partially explains the correlation between mass and frequency: light amino acids being typically encoded by highly degenerate codon families, with the exception of arginine. While degeneracy may be a factor in hard wiring the relationship between mass and frequency in proteomes, it does not provide a complete explanation. By examining extremophiles, we are able to show that this law weakens with temperature, likely due to protein stability considerations, thus the environment is essential.

Abstract
In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.